CLC Sequence Viewer 8.0Free
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CLC Sequence Viewer includes a number of features for doing basic bioinformatics analysis. You can create and edit alignments, work with interactive restriction site analysis, phylogenetics, or advanced DNA to protein translation, or you can use the integrated GenBank search options and many other features.
Bioinformatics features: Multiple alignment of DNA, RNA, and proteins , consensus sequence determination and management, conservation score along alignments, etc.